Contacts of the helix formed by residues 224 - 247 (chain A) in PDB entry 4LBD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A LEU* 3.6 28.6 + - + +
223A ASP* 1.3 70.4 + - - +
225A GLY* 1.3 64.4 + - - +
226A LEU 3.2 1.3 - - - -
227A TRP* 3.7 13.2 - - + +
228A ASP* 3.0 33.6 + - - +
403A GLU 4.8 1.3 - - - +
404A ILE* 4.5 1.3 - - - -
405A PRO* 3.3 41.7 - - + -
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Residues in contact with GLY 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A SER* 5.8 2.0 - - - -
223A ASP* 3.1 7.0 + - - -
224A LEU* 1.3 76.9 - - - +
226A LEU* 1.3 61.7 + - - +
228A ASP* 3.4 9.4 + - - +
229A LYS* 3.3 22.0 + - - +
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A THR* 3.9 21.1 - - + +
214A SER* 3.8 37.2 - - - +
223A ASP* 3.3 33.3 + - + +
224A LEU 3.2 0.2 - - - -
225A GLY* 1.3 78.1 - - - +
227A TRP* 1.3 56.5 + - - +
229A LYS* 3.4 7.6 + - + +
230A PHE* 2.9 28.8 + - - +
292A LEU* 5.8 3.6 - - + -
294A LEU* 4.4 11.5 - - + +
298A GLN* 3.6 28.3 - - + +
301A ASN* 4.2 4.9 - - + -
302A ALA* 4.0 17.1 - - + +
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Residues in contact with TRP 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A 961 3.9 12.8 - - + -
222A LEU* 3.9 8.3 - - + -
223A ASP 3.0 15.6 + - - +
224A LEU* 3.9 13.5 - - + +
225A GLY 3.4 0.4 - - - -
226A LEU* 1.3 75.9 - - - +
228A ASP* 1.3 72.1 + - - +
230A PHE* 3.6 31.0 - + - -
231A SER* 2.8 44.7 + - - -
302A ALA 3.2 34.7 + - - +
303A GLY* 4.3 4.9 - - - -
400A LEU* 3.7 18.6 - - + -
404A ILE* 3.6 40.3 - - + +
408A MET* 3.6 41.5 - - + -
409A PRO* 4.5 3.5 - - + +
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Residues in contact with ASP 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU* 3.0 22.8 + - - +
225A GLY* 3.7 8.9 - - - +
226A LEU 3.3 0.4 - - - -
227A TRP* 1.3 85.7 + - - +
229A LYS* 1.3 65.5 + - - +
231A SER* 3.0 17.3 + - - -
232A GLU* 3.0 15.6 + - - +
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Residues in contact with LYS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A TYR* 3.4 21.8 + - - -
225A GLY 3.3 10.8 + - - +
226A LEU* 3.9 11.0 - - + +
228A ASP* 1.3 79.7 - - - +
230A PHE* 1.3 61.4 + - - +
232A GLU* 3.2 37.4 + - - +
233A LEU* 3.2 30.5 + - + +
290A ASP* 3.2 24.2 + - - +
292A LEU* 3.8 21.8 - - + -
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Residues in contact with PHE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A 961 3.3 72.0 - + + -
226A LEU 2.9 17.9 + - - +
227A TRP* 3.6 39.3 - + - +
228A ASP 3.2 0.2 - - - -
229A LYS* 1.3 74.5 - - - +
231A SER* 1.3 59.5 + - - +
233A LEU* 3.2 7.0 + - - +
234A ALA* 2.9 28.0 + - + +
288A PHE* 3.7 26.9 - + - -
292A LEU* 5.6 2.4 - - + +
294A LEU* 5.8 2.0 - - + -
302A ALA* 4.1 16.8 - - + -
303A GLY* 5.4 0.2 - - - -
304A PHE* 3.5 25.6 - + - -
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Residues in contact with SER 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A TRP* 2.8 37.3 + - - -
228A ASP* 3.0 15.9 + - - -
230A PHE* 1.3 80.3 - - - +
232A GLU* 1.3 55.9 + - - +
234A ALA* 3.1 3.5 + - - +
235A THR* 2.9 35.6 + - - -
409A PRO* 3.7 31.6 - - - +
412A ILE* 3.8 10.2 - - - +
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ASP 3.0 18.2 + - - +
229A LYS* 3.2 44.7 + - - +
231A SER* 1.3 77.9 + - - +
233A LEU* 1.3 63.2 + - - +
235A THR* 3.5 6.0 + - - -
236A LYS* 3.2 49.2 + - - +
409A PRO* 5.4 0.9 - - - +
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A 961 3.9 21.8 - - - +
229A LYS* 3.2 27.0 + - + +
230A PHE* 3.2 8.3 + - - +
232A GLU* 1.3 82.4 - - - +
234A ALA* 1.3 60.1 + - - +
236A LYS* 3.2 16.4 + - + +
237A CYS* 3.0 27.7 + - - +
288A PHE* 3.6 24.9 - - + -
289A SER* 5.2 1.3 - - - -
290A ASP* 3.4 35.0 - - + +
292A LEU* 3.6 31.9 - - + -
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A 961 3.3 43.4 - - + -
230A PHE* 2.9 18.8 + - + +
231A SER* 3.6 5.8 - - - +
233A LEU* 1.3 74.7 - - - +
235A THR* 1.3 63.1 + - - +
237A CYS* 3.1 4.9 + - - +
238A ILE* 3.0 28.5 + - - +
271A LEU* 4.5 3.0 - - + +
412A ILE* 4.0 15.9 - - + -
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Residues in contact with THR 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A SER 2.9 19.0 + - - -
232A GLU* 3.6 7.5 - - - -
234A ALA* 1.3 74.9 - - - +
236A LYS* 1.3 65.6 + - + +
238A ILE* 3.2 20.6 + - - +
239A ILE* 3.2 18.7 + - + +
409A PRO* 3.6 24.0 - - + +
410A PRO* 6.5 0.4 - - + -
411A LEU* 3.6 29.1 - - + +
412A ILE* 3.8 6.5 - - - +
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Residues in contact with LYS 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A 961 6.0 0.2 - - - +
232A GLU* 3.2 41.6 + - - +
233A LEU* 3.2 18.8 + - + +
235A THR* 1.3 80.1 - - + +
237A CYS* 1.3 60.3 + - - +
239A ILE* 3.4 12.0 + - + +
240A LYS* 3.1 26.3 + - + +
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Residues in contact with CYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A 961 3.5 39.9 - - + -
201A PHE* 4.9 0.9 - - - -
233A LEU 3.0 13.2 + - - +
234A ALA 3.4 8.1 - - - +
236A LYS* 1.3 75.4 - - - +
238A ILE* 1.3 60.1 + - - +
240A LYS* 2.9 8.1 + - - +
241A ILE* 2.8 33.1 + - - +
271A LEU* 3.5 19.1 - - + -
274A ARG* 3.7 28.3 - - - -
289A SER* 5.6 0.9 - - - -
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Residues in contact with ILE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ALA* 3.0 15.9 + - + +
235A THR* 3.2 9.2 + - - +
237A CYS* 1.3 75.0 - - - +
239A ILE* 1.3 62.1 + - + +
241A ILE* 3.2 8.9 + - - +
242A VAL* 3.0 31.7 + - + +
267A CYS* 3.7 18.2 - - - -
271A LEU* 3.9 17.7 - - + -
411A LEU* 3.7 37.9 - - + +
412A ILE* 4.0 23.3 - - + -
415A MET* 4.0 17.3 - - + -
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Residues in contact with ILE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A THR* 3.2 17.0 + - + +
236A LYS* 3.6 12.1 - - + +
237A CYS 3.1 0.4 - - - -
238A ILE* 1.3 76.6 - - - +
240A LYS* 1.3 61.5 + - + +
242A VAL* 3.3 9.2 + - + +
243A GLU* 2.9 35.9 + - + +
411A LEU* 3.6 28.0 - - + -
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Residues in contact with LYS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU 3.7 14.5 + - - -
200A THR* 3.4 32.8 - - - +
236A LYS* 3.1 15.5 + - + +
237A CYS* 2.9 11.3 + - - +
239A ILE* 1.3 81.0 - - + +
241A ILE* 1.3 56.3 + - - +
243A GLU* 3.3 37.6 + - - +
244A PHE* 2.9 28.8 + - - +
274A ARG* 3.8 6.1 - - - +
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Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A CYS 2.8 11.9 + - - +
238A ILE* 3.2 7.6 + - - +
240A LYS* 1.3 74.3 - - - +
242A VAL* 1.3 61.7 + - + +
244A PHE* 3.1 11.5 + - + +
245A ALA* 2.8 28.1 + - + +
263A LEU* 3.9 15.0 - - + -
267A CYS* 3.9 25.1 - - - +
270A ILE* 3.6 49.6 - - + -
271A LEU* 3.5 34.3 - - + +
274A ARG* 3.9 16.4 - - - -
336A LEU* 5.5 0.2 - - + -
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Residues in contact with VAL 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ILE* 3.0 25.0 + - + +
239A ILE* 3.6 10.3 - - + +
241A ILE* 1.3 75.6 - - + +
243A GLU* 1.3 63.1 + - - +
245A ALA* 3.1 2.9 + - - +
246A LYS* 3.0 44.8 + - + +
263A LEU* 3.9 37.7 - - + -
267A CYS* 5.9 0.2 - - - -
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Residues in contact with GLU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU 4.3 3.1 - - - +
200A THR* 3.3 20.9 - - + +
239A ILE* 2.9 23.4 + - + +
240A LYS* 3.3 37.6 + - - +
242A VAL* 1.3 76.6 - - - +
244A PHE* 1.3 60.7 + - - +
246A LYS* 3.3 17.1 + - - +
247A ARG* 3.4 28.9 + - + +
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Residues in contact with PHE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A VAL* 4.0 6.7 - - + -
196A ALA* 3.6 21.8 - - + -
197A HIS* 3.7 27.4 - - + -
200A THR* 3.3 22.8 - - - +
240A LYS 2.9 13.0 + - - +
241A ILE* 3.4 8.1 - - + +
243A GLU* 1.3 73.3 - - - +
245A ALA* 1.3 68.6 + - + +
247A ARG* 3.1 17.6 + - - +
248A LEU* 3.3 44.9 + - + +
270A ILE* 5.4 10.8 - - + -
274A ARG* 4.2 9.9 - - - +
329A GLY* 3.4 24.5 - - - -
332A SER* 4.1 19.5 - - - -
333A ALA* 4.2 4.9 - - - -
336A LEU* 5.5 2.2 - - + -
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Residues in contact with ALA 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ILE* 2.8 14.3 + - + +
242A VAL 3.4 8.5 - - - +
244A PHE* 1.3 78.2 - - + +
246A LYS* 1.3 63.1 + - - +
248A LEU* 3.3 18.8 + - - +
251A PHE* 3.1 40.7 - - + +
263A LEU* 3.9 10.3 - - + -
336A LEU* 3.4 25.8 - - + -
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Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A VAL* 3.0 34.0 + - + +
243A GLU* 3.5 10.3 - - - +
244A PHE 3.2 0.4 - - - -
245A ALA* 1.3 77.6 - - - +
247A ARG* 1.3 60.5 + - + +
248A LEU 3.6 4.5 + - - +
251A PHE* 3.8 21.5 - - + -
252A THR* 3.5 25.4 + - - +
259A GLN* 3.5 20.0 - - - +
263A LEU* 5.6 1.6 - - - -
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Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS* 4.9 8.2 + - - +
195A LYS* 4.5 2.8 - - - +
196A ALA* 3.7 36.3 + - + +
199A GLU* 2.8 55.8 + - - +
200A THR* 4.8 2.9 - - - +
243A GLU* 3.4 29.4 + - + +
244A PHE* 3.1 8.1 + - - +
246A LYS* 1.3 76.3 - - + +
248A LEU* 1.3 63.5 + - - +
249A PRO* 3.4 9.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il